Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors.

The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.

Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein.

STING (stimulator of interferon genes) is a key regulator of innate immunity that has recently been recognized as a promising drug target. STING is activated by cyclic dinucleotides (CDNs) which eventually leads to expression of type I interferons and other cytokines. Factors underlying the affinity of various CDN analogues are poorly understood. Herein, we correlate structural biology, isothermal calorimetry (ITC) and computational modeling to elucidate factors contributing to binding of six CDNs-three pairs of natural (ribo) and fluorinated (2'-fluororibo) 3',3'-CDNs. X-ray structural analyses of six {STING:CDN} complexes did not offer any explanation for the different affinities of the studied ligands. ITC showed entropy/enthalpy compensation up to 25 kcal mol-1 for this set of similar ligands. The higher affinities of fluorinated analogues are explained with help of computational methods by smaller loss of entropy upon binding and by smaller strain (free) energy.

Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations.

Cyclic dinucleotides are second messengers in the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and inhibitor of nuclear factor-κB (IκB) kinase (IKK)/nuclear factor-κB (NFκB) signaling cascades. In this work, we describe an enzymatic preparation of 2'-5',3'-5'-cyclic dinucleotides (2'3'CDNs) with use of cyclic GMP-AMP synthases (cGAS) from human, mouse, and chicken. We profile substrate specificity of these enzymes by employing a small library of nucleotide-5'-triphosphate (NTP) analogues and use them to prepare 33 2'3'CDNs. We also determine affinity of these CDNs to five different STING haplotypes in cell-based and biochemical assays and describe properties needed for their optimal activity toward all STING haplotypes. Next, we study their effect on cytokine and chemokine induction by human peripheral blood mononuclear cells (PBMCs) and evaluate their cytotoxic effect on monocytes. Additionally, we report X-ray crystal structures of two new CDNs bound to STING protein and discuss structure-activity relationship by using quantum and molecular mechanical (QM/MM) computational modeling.

Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-ß (Aß), metal-Aß, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

Interactions of small gold clusters, Aun (n=1-3), with graphyne: theoretical investigation.

The interactions of gold atom and clusters (Au2 and Au3) with the active sites of graphyne (GY) have been investigated using density functional theory (PBE, PBE-D3, and B3LYP-D3). In order to compare performance of DFT functional (BP86, PBE, TPSSh, B3LYP, PBE-D3, TPSSh-D3, and B3LYP-D3), the interactions of Au2 with various functional groups such as -sp, -sp(2) and aromatic sp(2) carbon atoms, -sp, -sp(2) and aromatic sp(2)-bonds have been investigated and also compared with the ab initio MP2 results. Additionally, the nature of interactions for graphyne-Au2 complexes are interpreted by means of the natural bond orbital (NBO), the quantum theory of atoms in molecules (QTAIM) and energy decomposition analysis (EDA) and compared with those of related graphene-Au2. This study suggests that graphyne shows complex behavior in comparison to those of graphene and could also be useful in modeling of the next generation electronic devices.

Theoretical investigation on antioxidant activity of bromophenols from the marine red alga Rhodomela confervoides: H-atom vs electron transfer mechanism.

Bromophenols are known as antioxidant radical scavengers for some biomolecules such as those in marine red alga. Full understanding of the role played by bromophenols requires detailed knowledge of the radical scavenging activities in probable pathways, a focus of ongoing research. To gain detailed insight into two suggested pathways, H-atom transfer and electron transfer, theoretical studies employing first principle quantum mechanical calculations have been carried out on selected bromophenols. Detailed investigation of the aforementioned routes revealed that upon H-atom abstraction or the electron transfer process, bromophenols cause an increase in radical species in which the unpaired electron appears to be delocalized as much as possible over the whole aromatic ring, especially in the bromine substituent. The O-H bond dissociation energies (BDEs) and ionization potential energies (IPs) are reported at the B3LYP level of theory, providing the first complete series of BDEs and IPs for bromophenols. The observations are compared to those of other antioxidants for which BDEs and IPs have been previously obtained.

Interactions of coinage metal clusters with histidine and their effects on histidine acidity; theoretical investigation.

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M(3) clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M(3) clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H···M and O-H···M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next step, the effects of Au, Ag and Cu metal clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine was compared with the acidity of its Au(3)-, Ag(3)- and Cu(3)-complexed species. Results indicate that upon complexation with M(3) clusters (at 298 K), the gas-phase acidity (GPA) of histidine varies from 339.5 to 312.3, 315.0, and 313.7 kcal mol(-1) for Au(3)-, Ag(3)- and Cu(3)-His complexes, respectively (i.e., its dissociation becomes much less endothermic). These values indicate that a weak organic acid can be converted to a super acid when it is complexed with metal clusters. Also, in order to investigate the acidity value of the imidazole moiety in histidine, histidine methyl ester (His-OMe) was selected. Similarly, the acidity of this compound was compared with the acidity of their Au(3), Ag(3) and Cu(3)-complexed species. After complexation with M(3) clusters at 298 K, the gas-phase acidity (GPA) of His-OMe varies from 333.0 to 280.0, 304.2 and 291.5 kcal mol(-1), respectively. Moreover, pK(a) values were determined in water for isolated and complexed species of His and His-OMe. The resulting pK(a) values were found to decrease upon complexation with M(3) clusters.

DFT study of the interaction of cytidine and 2'-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond.

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li(+), Na(+), and K(+) with cytidine and 2'-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li(+) to Na(+) and K(+) for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2'-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1-C1' bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids.